uu.seUppsala University Publications
Change search
ReferencesLink to record
Permanent link

Direct link
Deleterious amino acid polymorphisms in Arabidopsis thaliana and rice.
2010 (English)In: Theoretical and Applied Genetics, ISSN 0040-5752, E-ISSN 1432-2242, Vol. 121, no 1, 157-68 p.Article in journal (Refereed) Published
Abstract [en]

Plant genetic diversity has been mainly investigated with neutral markers, but large-scale DNA sequencing projects now enable the identification and analysis of different classes of genetic polymorphisms, such as non-synonymous single nucleotide polymorphisms (nsSNPs) in protein coding sequences. Using the SIFT and MAPP programs to predict whether nsSNPs are tolerated (i.e., effectively neutral) or deleterious for protein function, genome-wide nsSNP data from Arabidopsis thaliana and rice were analyzed. In both species, about 20% of polymorphic sites with nsSNPs were classified as deleterious; they segregate at lower allele frequencies than tolerated nsSNPs due to purifying selection. Furthermore, A. thaliana accessions from marginal populations show a higher relative proportion of deleterious nsSNPs, which likely reflects differential selection or demographic effects in subpopulations. To evaluate the sensitivity of predictions, genes from model and crop plants with known functional effects of nsSNPs were inferred with the algorithms. The programs predicted about 70% of nsSNPs correctly as tolerated or deleterious, i.e., as having a functional effect. Forward-in-time simulations of bottleneck and domestication models indicated a high power to detect demographic effects on nsSNP frequencies in sufficiently large datasets. The results indicate that nsSNPs are useful markers for analyzing genetic diversity in plant genetic resources and breeding populations to infer natural/artificial selection and genetic drift.

Place, publisher, year, edition, pages
2010. Vol. 121, no 1, 157-68 p.
National Category
Evolutionary Biology
URN: urn:nbn:se:uu:diva-207312DOI: 10.1007/s00122-010-1299-4PubMedID: 20198468OAI: oai:DiVA.org:uu-207312DiVA: diva2:647761
Available from: 2013-09-12 Created: 2013-09-12 Last updated: 2013-09-12

Open Access in DiVA

No full text

Other links

Publisher's full textPubMed

Search in DiVA

By author/editor
Günther, Torsten
In the same journal
Theoretical and Applied Genetics
Evolutionary Biology

Search outside of DiVA

GoogleGoogle Scholar
The number of downloads is the sum of all downloads of full texts. It may include eg previous versions that are now no longer available

Altmetric score

Total: 151 hits
ReferencesLink to record
Permanent link

Direct link